{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,12]],"date-time":"2024-09-12T15:53:12Z","timestamp":1726156392498},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2201,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Finding functionally analogous enzymes based on the local structures of active sites is an important problem. Conventional methods use templates of local structures to search for analogous sites, but their performance depends on the selection of atoms for inclusion in the templates.<\/jats:p>\n               <jats:p>Results: The automatic selection of atoms so that site matches can be discriminated from mismatches. The algorithm provides not only good predictions, but also some insights into which atoms are important for the prediction. Our experimental results suggest that the metric learning automatically provides more effective templates than those whose atoms are selected manually.<\/jats:p>\n               <jats:p>Availability: Online software is available at http:\/\/www.net-machine.net\/\u223ckato\/lpmetric1\/<\/jats:p>\n               <jats:p>Contact: \u00a0kato-tsuyoshi@k.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq519","type":"journal-article","created":{"date-parts":[[2010,9,25]],"date-time":"2010-09-25T00:18:28Z","timestamp":1285373908000},"page":"2698-2704","source":"Crossref","is-referenced-by-count":19,"title":["Metric learning for enzyme active-site search"],"prefix":"10.1093","volume":"26","author":[{"given":"Tsuyoshi","family":"Kato","sequence":"first","affiliation":[{"name":"1 GSFS, University of Tokyo, 5-1-5 Kashiwahoha, Kashiwa, Chiba 277-8561 and 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"},{"name":"1 GSFS, University of Tokyo, 5-1-5 Kashiwahoha, Kashiwa, Chiba 277-8561 and 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"}]},{"given":"Nozomi","family":"Nagano","sequence":"additional","affiliation":[{"name":"1 GSFS, University of Tokyo, 5-1-5 Kashiwahoha, Kashiwa, Chiba 277-8561 and 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan"}]}],"member":"286","published-online":{"date-parts":[[2010,9,23]]},"reference":[{"key":"2023012507544806000_B1","volume-title":"Methods of Information Geometry.","author":"Amari","year":"2000"},{"issue":"Web Server issue","key":"2023012507544806000_B2","doi-asserted-by":"crossref","first-page":"W529","DOI":"10.1093\/nar\/gkq399","article-title":"Consurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids","volume":"38","author":"Ashkenazy","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012507544806000_B3","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1093\/bioinformatics\/btg226","article-title":"An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis","volume":"19","author":"Barker","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507544806000_B4","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/S0022-2836(02)01036-7","article-title":"Analysis of catalytic residues in enzyme active sites","volume":"324","author":"Bartlett","year":"2002","journal-title":"J. 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